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3. LongPolyASE: an end-to-end framework for allele-specific gene and isoform analysis in polyploids using long-read RNA-seqNadja Franziska Nolte, Kristina Gruden, Marko Petek, 2026, original scientific article Abstract: Background Allele-specific expression analysis can reveal cis-regulatory differences (e.g., promoter variants, epigenetic changes) that cause imbalanced gene expression between haplotypes. Haplotype-resolved reference genomes and long-read RNA sequencing enable allele-specific expression analysis at gene and isoform-levels. However, existing tools are largely restricted to short-read RNA sequencing data and diploid organisms. Results We developed LongPolyASE, an end-to-end computational framework for allele-specific gene and isoform expression analysis in diploid and polyploid organisms using long-read RNA sequencing, consisting of three components: Syntelogfinder, for identifying syntenic gene relationships and annotation inconsistencies; longrnaseq, for novel isoform discovery and haplotype-level quantification; and PolyASE, for statistical testing and visualization of allelic imbalance and isoform usage. We applied LongPolyASE to diploid rice, autotetraploid potato, allotetraploid rapeseed, and allooctoploid strawberry using Oxford Nanopore and PacBio long-read RNA-seq. The framework enabled identification of cis-regulatory variation, tissue-specific trans-regulatory effects, differential isoform usage, and haplotype-specific splicing differences. In addition, it facilitated the discovery of novel transcripts and genes with potential functional relevance in plant development. Conclusions LongPolyASE addresses a key methodological gap by enabling allele-specific expression analysis in polyploid organisms using long-read RNA sequencing. By combining haplotype-aware quantification with isoform-level resolution in a reproducible workflow, the framework provides a practical tool for plant researchers working with complex genomes. Its application to crop species highlights its potential to support the identification of regulatory variation and candidate targets for plant breeding.
Keywords: allele-specific expression analysis, polyploids, long-read RNA-seq, isoform expression, gene expression
Published in DiRROS: 03.08.2026; Views: 220; Downloads: 128
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4. Delavnica izdelave NRRP : naravoslovje in tehnikaMaja Zagorščak, Marko Petek, Uroš Kunaver, Petra Durini, Jože Hladnik, 2025, other monographs and other completed works Keywords: NRRP, izdelava, naravoslovje, tehnika
Published in DiRROS: 03.06.2026; Views: 431; Downloads: 327
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5. Metadata from: Combining short- and long-read transcriptomes for targeted enzyme discoveryMojca Juteršek, Marko Petek, Špela Baebler, 2025, research data Keywords: genes, enzymatic activity, transcriptomics, metabolic pathways, allelic variation, isoform expression, biotechnological tools
Published in DiRROS: 20.03.2026; Views: 486; Downloads: 458
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6. White paper: standards for handling and analyzing plant pan-genomesMarc C. Heuermann, Pedro Miguel Barros, Sebastian Beier, Tim Godec, Kristina Gruden, Nadja Franziska Nolte, Marko Petek, Maja Zagorščak, 2025, review article Abstract: Plant pan-genomes, which aggregate genomic sequences and annotations from multiple individuals of a species, have emerged as transformative tools for understanding genetic diversity, adaptation, and evolutionary dynamics. Super-pan-genomes, extending across species boundaries, further enable comparative analyses of clades or genera, bridging breeding applications with evolutionary insights (Shang et al., 2022; Li et al., 2023a). However, the absence of standardized practices for data generation, analysis, and sharing hinders reproducibility and interoperability. This white paper presents a harmonized framework developed by the ELIXIR E-PAN consortium, addressing nomenclature, quality control (QC), data formats, visualization, and community practices. By adopting these guidelines, researchers can enhance FAIR (Findable, Accessible, Interoperable, Reusable) compliance, foster collaboration, and accelerate translational applications in crop improvement and evolutionary biology.
Keywords: plant pan-genome, white paper, standards, quality control
Published in DiRROS: 24.02.2026; Views: 596; Downloads: 311
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7. Identification and cultivation of biotechnologically relevant microalgal and cyanobacterial species isolated from Sečovlje salt pans, SloveniaEylem Atak, Petra Tavčar Verdev, Marko Petek, Anna Coll Rius, Daniel Bosch, Marko Dolinar, Viktoriia Komarysta, Neli Glavaš, Ana Rotter, 2026, original scientific article Keywords: culture conditions, halophilic organisms, hypersaline environment, identification of microorganisms, shotgun metagenomics, photosynthetic microorganisms
Published in DiRROS: 28.01.2026; Views: 627; Downloads: 471
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8. Signalling network construction for modelling plant defence responseDragana Miljković, Tjaša Stare, Igor Mozetič, Vid Podpečan, Marko Petek, Kamil Witek, Marina Dermastia, Nada Lavrač, Kristina Gruden, 2012, original scientific article Published in DiRROS: 26.11.2025; Views: 853; Downloads: 434
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9. Evaluating plant growth–defense trade-offs by modelingthe interaction between primary and secondary metabolismJan Zrimec, Sandra Correo, Maja Zagorščak, Marko Petek, Carissa Bleker, Katja Stare, Christian Schuy, Sophia Sonnewald, Kristina Gruden, Zoran Nikoloski, 2025, original scientific article Abstract: Understanding the molecular mechanisms behind plant response to stress can enhancebreeding strategies and help us design crop varieties with improved stress tolerance,yield, and quality. To investigate resource redistribution from growth- to defense-relatedprocesses in an essential tuber crop, potato, here we generate a large-scale compartmen-talized genome-scale metabolic model (GEM), potato-GEM. Apart from a large-scalereconstruction of primary metabolism, the model includes the full known potato sec-ondary metabolism, spanning over 566 reactions that facilitate the biosynthesis of 182distinct potato secondary metabolites. Constraint-based modeling identifies that theactivation of the largest amount of secondary (defense) pathways occurs at a decreaseof the relative growth rate of potato leaf, due to the costs incurred by defense. We thenobtain transcriptomics data from experiments exposing potato leaves to two bioticstress scenarios, a herbivore and a viral pathogen, and apply them as constraints toproduce condition-specific models. We show that these models recapitulate experimen-tally observed decreases in relative growth rates under treatment as well as changes inmetabolite levels between treatments, enabling us to pinpoint the metabolic rewiringunderlying growth–defense trade-offs. Potato- GEM thus presents a useful resource tostudy and broaden our understanding of potato and general plant defense responsesunder stress conditions.
Keywords: systems biology, constraint-based metabolic modeling, growth-defence trade-offs, secondary metabolism
Published in DiRROS: 24.09.2025; Views: 1308; Downloads: 602
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10. A comprehensive guide to potato transcriptome assemblyMaja Zagorščak, Marko Petek, 2021, independent scientific component part or a chapter in a monograph Abstract: We have witnessed a rapid advancement in high-throughput genome sequencing and the maturation of long-read technologies. However, an accurate assembly of polyploid potato genomes still remains challenging. Sequencing the double-monoploid genome of Solanum tuberosum Group Phureja (Xu et al., Nature 475:189–195, 2011) has enabled functional studies of polyploid potato cultivars using RNA sequencing (RNA-Seq) technologies, although with the limitation of not covering cultivar-specific gene expression. The accumulated RNA-Seq datasets from these cultivars can be leveraged to assemble tetraploid potato transcriptomes that enable the analysis of genes that are not limited to reference genome annotations. To increase transcriptomes’ quality, short-read assemblies are nowadays complemented with full-length transcriptome sequencing using Pacific Biosciences or Oxford Nanopore platforms. In this chapter we give a detailed guide on a pipeline for de novo transcriptome assembly of polyploid potato genotypes and their integration into a pan-transcriptome.
Published in DiRROS: 06.08.2025; Views: 859; Downloads: 531
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